Wednesday, June 13, 2007

Blog for the 2nd Week

Thank you for a very good Journal Club today.
Please put your blog for the second week here. Remember to post how your skills, content knowledge, and self confidence are growing!

Marti

10 comments:

Alexander Nguyen said...

Well, Marti, this week has been going on splendidly. I've learned a lot from my mentors in the physiology rotation. Learning from them has been a joy and an adventure at the same time.

On Monday, I reported to Dr. Camenisch our preliminary findings in the first trial of the immunohistochemistries. He was very impressed, and Mark and I decided to set up another run. I've been also assisting Mark on various other procedures, such as DNA extraction, explantation of organs, and still reading research papers. I guess that they were very crucial to research. Currently, we're at our 2nd trial and planning to perform the third trial if everything seems to be going as planned. My experience there has been fun and education simultaneously. In my spare time, I've also been helping out running gels and PCR, so my lab skills are improving significantly, and they're teaching me tricks to a lot of techniques I've had to struggle with.

Tiffany said...

Hi!
This week I've seen a considerable increase in the responsibilities that Gladys has given me. I am much more confident in performing certain procedures, such as making gels for Western Blots and carrying out the specific steps of protein transfer. I've learned that taking detailed notes on the steps is very important; at first I thought that I could remember everything, but this is not the case! I have found that my notes are an invaluable resource and they help me perfect my technique.
So far Gladys has been introducing me to the intricate process of determining neurotransmitters. We use a machine to see a graph of the concentrations of neurotransmitters versus time, and any peaks in the line graph indicate the presence of a specific neurotransmitter. In this way, we can analyze the concentrations of serotonin before and after injecting metabolites and determine the effect that the metabolites of ecstasy have on the rats that were sacrificed for this experiment.
Gladys told me today that the rats for the second round of experiments will come in next week. I am looking forward to working with animals and seeing the beginning processes of Gladys' experiment; after all, when I started this internship, I was able to observe what happened after the rats had already had brain surgery and were sacrificed for their brain tissue.
I think that next week will bring more excitement!

Andrew said...

This week is a week full of UPs...and some DOWNs. The ups were a plus because these include my new found responsiblity in the lab and all the things I get to do by myself. I feel more and more independent in the lab, even if I did mess up occasionally. I have to learn from those mistakes. My week consisted of assisting my mentors with what they needed and performing assays that were eventually repeated thorughout the week just for practice. I have felt more confident with my abilites in the lab and the abilities to communicate with fellow interns.

Highlight of the week: Talking to mon-Ning's lover and our joyful college student/restaurant worker- LBD (AKA Longboard Dude)

Journal club was amazing. I felt like there were things that I could have done better and there are things that were just fine. I guess I was a little repetitive but I was just trying to get the main point across. So the most important thing for me this week is performing some of the experiments. I was expected to do most things by myself like feed my cells. I really am glad that I have this experience and I hope that the next weeks will bring more joyful times.

Mon-Ning said...

Aloha,

It’s the second week of interning and it’s getting pretty intense. Since my mentor is out of the country, lab tech and grad mentor Natalia has taken over in educating me on the basics of lab research and how to get around the lab. Natalia is awesome and really nice. She spends a lot of time explaining everything out and she’s really patient with just about everything

The week started out kind of low and it got more mind stimulating as the week went on. It was sort of a time-to-do-stuff-on-your-own week, which was pretty awesome. My assignment for the week was to grow up my mysterious dog killing fungus in order to look at it morphologically and genetically. I had to make two different medias and pour two different kinds of plates. I used the ordinary Petri dish for my growth medias and a two 24 well plate for my genetic research medias.

Since, no one really knows what kind of fungus, my fungus is we had to use tons of different medias for growth. I stirred up some oatmeal agar, potato dextrose agar, two types of yeast agar, Sabouraud’s agar, and malt extract agar. Then I placed a little piece of the fungus on the middle of each plate for growth. Natalia suggested that I put the different plates in different environments. So I stuck two of each of the medias into a lighted 25ºC room, a dark 27ºC cabinet, and a 37ºC cabinet. So far there isn’t much progress on the growth of any of the plates.

For my two 24 well plates I used two different types of liquid media, which I’m not really sure what they are, but Natalia just said that one is the standard solution and the other is a lot richer than the last. I also placed a little piece of my fungus in each well, but only stuck the 24 well plates in the dark cabinet set for 27ºC. There seems to be no growth here as well, but I seem to be getting some bacteria growth inside a few of the wells, so there will be future hypothesis on why this happened.

The rest of the week was sort of different types of prep work for future experiments and waiting to see some growth on the different plates. It was also a lot of time dedicated into the other projects that teacher-intern Vicki is working on. I did some PCR on the soil sample DNAs, since we seem to be having troubles just trying to isolate the fungal DNA in the samples. I also ran gels on them, with not a lot of luck in isolating just the assumed fungal DNA. Right now we’re still trying different approaches in tackling the problem such as changing the temperatures, running the PCR longer, and adding different chemical solutions to enhance the PCR reaction.

Well, that’s the update of this week and I’m out!
Mon-Ning

Shiana said...

Illumination

It seems the longer we’ve all been interns, the closer we’ve all grown. We have gone from arranging to meet at lunch every day to creating our own TV show to even planning weekend get-togethers. Being among a group so interested in research and science in general is wonderful. This past week for me has continued to entail meeting many new faces and making new friends. I have had the chance to talk to UMC interns, Bio Academy interns and its teachers, and a professor, Dr. Karen McGinnis, from the plant sciences department.

While at first the research project that I was to eventually conduct on my own and independently was hard for me to fully comprehend, through asking a great many questions and double-checking concepts (sometimes thrice-checking) with my mentor, I have been able to piece together the big picture of my project as well as what is occurring at the molecular level in every lab procedure that my mentor and I have conducted so far. The terminology that my field of research involves has become easier for me to understand, which helps me immensely in reading through my research papers and additional articles online. I am continuing to do research to find out smaller details about cell processes and the chemicals, proteins, and enzymes involved. My confidence in the lab, now that I have familiarized myself with my surroundings, has increased pleasantly.

My mentor took the time out last weekend to draft a schedule for what I would be occupied with during the rest of my internship and this week was designated for learning technique and reading the principles of procedures and about a variety of other related concepts. This meant that I was to mostly watch my mentor and take careful notes on how things were done. Meanwhile, I was able to learn how to create agarose solutions and adjust buffer concentrations, as well as learn about protein gels (though proteins are not a part of my project). By the time Thursday swung about and we met the second time with Dr. Monks, our lab’s principle investigator, my mentor’s confidence in me had grown and she allowed me to start conducting my experiment by myself ahead of schedule.

As a summary of the beginning of my project, this week my mentor and I prepared our control vector that contained Prx III without any mutation. We also performed mutagenesis of Cys 108 by replacing it with Ser (abbreviated C108S) and C229S using our four mutagenesis primers that we ordered last week. Next week when I take over my project, I will use most of the same methods I saw this week to create three vectors with only C108S and C229S mutations, and then one with both mutations. When we arrive at this point, we will analyze the altered function of Prx III with its double mutations compared to a normal Prx III by putting Prx III back into a live cell.

Kim said...

This week Aysen and I have continued doing protein and DNA purifications, ligations, and digestions, but they are no longer just procedures to me. We run at least three protocols at once, but the initial daze and confusion, the blind pipetting and such has subsided. Last week's focus for me was understanding individual steps of the protocol - after the buffer add what; why do we have a secondary antibody? I'm still learning more of every step, but now I'm stepping back - stepping back in a sense that I can look up at the bigger picture, the goals, the significance of result, where all those little steps add up to. We are studying the Enteropathogenic and Enterohemorrhagic strains of E. Coli specifically the flagella of each. Does the flagella have an affinity to mucin? Specifically, does each monomer of the flagella have an affinity to the mucin - and further, does a section of each flagellin's DNA also have a reaction to mucin? Mucins are a component of mucus, secreted as a line of defense against pathogens, such as EPEC and EHEC strains of E.coli. We test each structure of the flagella with Western blots and immunofluorescence to determine affinity. We are also digesting, purifying, and ligating plasmids to take up a DNA insert that codes for the flagella. After we have ascertained the plasmid has taken up the insert, we will send it to be sequenced and hopefully will find that the genes and the insert can be expressed properly. I'm excited to see what we'll accomplish next week!

Logan said...

This week has passed in a haze of activity. Brianna and I were so busy with 3 and sometimes 4 projects occurring simultaneously, we had to sit down and run through our progress with each one at least twice a day. In the times when I wasn't hurrying around the lab experiencing my own successes and failures (science is 95% failure, right?) I was growing closer to all of the other interns. I think all of us being brought together under our common interest in the sciences is one of the best things that will happen to me this summer. We are preparing ourselves for a high-powered future in the sciences and making connections and networking not only with others in the field, but between ourselves so as to form a sort of support group. Now support group sounds like we're all in dire need of help, which I don't think is the case at this point, so I think "Beastly Band of Bio5 (and KEYS) Interns" might better describe us (and beastly is a good thing, in case you were wondering).

SO, in the lab this week I began my own project. This consists of characterizing the promoter region of the Aedes Aegypti elongation factor 1 alpha-encoding gene. I started off with some mild failure. The first PCR I ran with the primers we ordered to isolate the first portion of the possible promoter region did not yield desired products. I needed to change the conditions of the PCR. This included increasing the annealing temperature and increasing the extension time in order to accomodate the portion of DNA I was attempting to amplify. The second time was a complete success, and I performed the PCR a third time just to ensure that I would have sufficient DNA for the rest of the project. Through band prep, ligation and transformation throughout the week by Friday I had cultures to grow over the weekend that should be chock full of the portion fo teh elongation factor I want. I have PLENTY more to do with my project.

Jun felt that one project of thsi type wasn't quite enough for me, so he agve me a SECOND one that is very similar but involving the 5G1 gene, which encodes for trypsins in the midgut of Aedes Aegypti mosquitoes. I've begun working on that, and hopefully I will have more success with both of the projects I now have on my plate.

I've also been helping Brianna with the thigns she is working on. These include: a luciferase assay involving S2 cells (luciferase is the reporter gene used in almost every project in my lab currently) and a project putting sense and antisense in the same vector side by side meant to test RNAi. To say the least, we've been BUSY.

As you can see Marti, my knowledge and skills have grown exponentially. I feel bad when I try to explain to my friends exactly what I'm doing in the lab, because I have to define nearly every other term I use. I can now perform procedures completely on my own without even having to ask someone where some reagant is or check how to work some machine. That alone is an indicator of the confidence I have acquired in the lab. This experience is so pleasantly beneficial and I hope it stays that way.

Daniel said...

Hello Interns,

First and foremost I would like to apologize that I was unable to post a blog earlier last week! I have been extremely inundated with all my summer activities nonetheless this week should be pleasantly relaxing and allow for me to blog and post more often.

Ok here is another one of my quotes-->

Try not to become a man of success but a man of value.
-Albert Einstein

My time in the laboratory this past week has been moderately interesting! After learning how to process Deoxyribonucleic Acid Extractions (DNA) from animal tissues (i.e. Flat Tale Horned Lizards) my mentor has finally unleashed my glory into the field of “actual” lab work. I have taken the skills; such as pipetting, I have gained from the launch of this internship and have incorporated them into my lab work today.

I am self-confident in my abilities to do Extractions and do them well, by way of following the “Handy- Dandy Notebook” with all the step by step instructions. In addition, I also believe that I am able to do Extractions in my sleep since I have processed them so many times! (Ha-ha)

Learning is the key to success in life and this internship! My mentor Tony has taught me a wealth of knowledge this is indispensable. Tony has been able to give me more and more responsibility in the laboratory and for that reason I am extremely grateful. I heed my mentor’ words of wisdom daily and only improve day after day in the lab.

Now as I bring this blog to a close remember you are all very valuable and knowledgeable to your respected laboratories, keep learning and good luck in pursuing your independent research projects.

-Daniel

Greg Reida said...

I too would like to apologize for not being able to blog last week. My Internet wasn't working this weekend and I just recently got it up and working. However, I must admit that blogging completely escaped my mind until this morning when Daniel reminded me about it. Any ways here goes:

Just like every other week this one started on a Monday and ended on a Friday. But it turned out that this week would quite paradoxical. How could one expect to be left alone in a lab working with samples that account for over 10 years of research all alone just after two weeks? Sure Daniel and I have been running countless DNA extractions, PCRs, and gels on a variety of creatures, (I'm talking Lions, and tigers, and bears! Oh, my!) but so far we have always been under the watchful eye of our mentors. I honestly didn't think that I was ready for the challenge of working alone but Tony had enough confidence for the both of us.

Luckily for me I didn't mess up this week thanks to Daniel, Demetre, Tony, and of course my handy dandy notebook. I guess this means I still have a job. At least for another week =P


P.S. I am really sorry I didn't get this blog in on time. I would like to thank Daniel for reminding me this morning and Alex for reminding me once I finally got my Internet back up and working.
Moreover since Dan has been putting quotes at the beginning of his blog entries I thought it would be fitting for me to end mine with a quote.

“Who has confidence in himself will gain the confidence of others.”

`Leib Lazarow quote

Coincidentally this too is paradoxical. Because our mentors had such great confidence in us me and Daniel were able to perform fantastically this week far above my own expectations.

Anonymous said...

I can see that the skills are growing exponentially and the new knowledge is seeping out of the brains. I appreciate the curiosity and willingness to interact so effectively with the faculty.